The captain was charged in a 17-count indictment, one count for each of the passengers that died when the vessel sank.
A total of 31 passengers were on board the duck boat when strong winds sank the boat, causing one of the deadliest US tourist tragedies in recent years.
According to Reuters, the captain is also accused of not assessing the weather properly, not instructing passengers to use personal flotation devices, or head for shore and prepare to abandon ship.
The captain now faces a possible sentence in federal prison without parole, in addition to a $250,000 fine.
At least 13 people have drowned after a tourist 'duck boat' sank during a storm on a lake in Missouri. As Missouri Governor Michael Parson informed, authorities are continuing the search for other missing victims.
Earlier, a contractor hired to inspect the duck boats, Steven Paul, said that he had seen a problem in the sunken boat that could have caused problems and informed the operator. Steven Paul examined the boat in August 2017 and found a problem with the exhaust which was in front of the vessel. As he said, the exhaust needs to come out past the passenger compartment.
Moreover, families of duck boat victims have filed lawsuit seeking $100 million in damages. According to the lawsuit, the fatal accident was caused by "unacceptable ignorance of safety by the Duck Boat industry."
The families also called the authorities to ban duck boats, as the families' attorneys indicated 26 deaths linked to six previous duck boat accidents.
Finally, in NTSB's preliminary report of the incident, it is noted that at the time of the incident, there were forecasts for thunderstorms in the area, while the ship experienced winds of over 70 mph. At that time, the 'Stretch Duck 7' was carrying 31 persons: 29 passengers and two crewmembers. The vessel sank in approximately 15 feet of water and came to rest on the lake floor at a depth of 70 feet. Seventeen persons died, including one crewmember.